Microbiology Lecture Notes PDF

MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 Class Gammaproteobacteria IJSEM (International Journal of Systematic & Evolutionary Microbiology) Order...

MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 Class Gammaproteobacteria IJSEM (International Journal of Systematic & Evolutionary Microbiology) Order Enterobacteriales ➔ Official publication of record for taxonomy and Family Enterobacteriaceae classification of Bacteria, Archaea, and microbial eukaryotes Genus Escherichia ◆ Before naming the microorganism it should be published first Species Coli Table 1: Taxonomic Ranks of the Bacterium Escherichia CHARACTERIZATION AND IDENTIFICATION Coli Why do microorganism change genus due to ➔ Involves the study, not of a single cell, but of a new discovery population of identical cells ○ That this microorganism is more ➔ Prerequisites: pure culture related to another organism REASONS FOR DOING CHARACTERIZATION First largest group domain ○ In organisms there can be three ➔ Identification purposes domain ➔ Comparison with other organisms PCOFGS (smallest doman) ➔ Exploit characteristics which may be beneficial (3) PRINCIPLES OF NOMENCLATURE 1.4 AN INTRODUCTION TO MICROBIAL ➔ Each distinct kind of organism is designated as LIFE a __ ➔ All cells fall into one of three major groups: ➔ List of species of prokaryotes Bacteria, Archaea, or Eukarya ◆ Bergey’s Manual of Systematic ➔ These three major cell lineages are called Bacteriology domains and all known cellular organism ◆ Bergey’s Manual of Determinative belong to one of these three domain Bacteriology ◆ Both are standard book for prokaryotes (always updated) ➔ These books act as standard references for identifying and classifying different prokaryotes ◆ Do not just rely on morphological (phenotype) but also molecular RULES FOR NAMING BACTERIA BACTERIA ➔ International code for the Nomenclature of ➔ Among the Bacteria, 30 major phylogenetic Bacteria (1991) lineages (called phylum) have at least one QUESTIONS ON NOMENCLATURE species that has been grown in culture, though many more pyla exist which remain largely ➔ International Journal of Systematic Bacteriology uncharacterized (IJSB) ◆ Largely remain uncharacterized. ◆ Question will be addressed to IJSB ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 8 MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ➔ More than 90% of cultivated bacteria belong to one of only four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. ➔ In figure A. major phyla that have cultivated (growth in lab), ◆ Majority is proteobacteria ◆ More than 80 bacterium phyla ➔ Figure B. cultured green bars those that are known through 16S rRNA gene sequence ➔ Majority of microorganism are known through 16S but not all are culturable Five major archaeal phyla ◆ Maybe half culturable Archaea are nearly as numerous as bacteria ➔ Types of species = pure culture but far fewer archaea cultivated ➔ Proteobacteria Archaea can form major 4 branches ◆ Gamma, alpha, beta, delta (under ○ Euryarchaeota, DPANN, TACK, Asgard phylum of proteobacteria) archaea EUKARYA ➔ Plants, animals, and fungi are the most well-known groups of Eukarya. ➔ These groups are phylogenetically relatively young compared with Bacteria and Archaea ➔ The major lineages of Eukarya are traditionally called kingdoms instead of phyla. ◆ Kingdom for eukarya ➔ There are at least six kingdoms of Eukarya, and this diverse domain contains microorganisms as well as plants and animals. ARCHAEA ➔ Like Bacteria, Archaea also have a prokaryotic cell structure. ➔ The domain Archaea consists of five described phyla: Euryarchaeota, Crenarchaeota, Thaumarcheota, Nanoarchaeota, and Korarcheota ➔ Archaea have historically been associated with extreme environments; the first isolates came from hot, salty, or acidic sites. ➔ But not all Archaea are extremophiles. ◆ Meaning they can thrive normal condition (room temperature, neutral Colors are used to identify the super groups pH) in the tree. ➔ Archaea are also notable in that this domain Dash lines indicates primary endosymbiosis lacks any known disease-causing (pathogenic ○ One cell has engulf another cell or parasitic) species of plants or animals. Secondary endosymbiosis ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 9 MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ○ Product of endosymbiosis has immediately converted to mRNA+ engulfed again Genome can be DNA or RNA (single or double stranded) ○ Class V and VI only eukaryotic VIRUSES All classes goal is to form mRNA to Viruses are not on the tree of life, and for a compliment the negative strand ➔ variety of reasons, it can be argued that they Class one and seven double stranded DNA are not truly alive. and positive and negative strand = it will only Although viruses can replicate- a hallmark of use the negative strand to transcribe the ➔ cells- viruses are obligate parasites that can mRNA only replicate within the cytoplasm of a host Class II has single stranded positive strand cell. virus or genome = if the positive and positive strand compliment it will produce negative ◆ Depended on host replication strand thus making the dsDNA intermediate ◆ Transfer genome to host allows to replicate (replicative form) Viruses are not cells Class four genome can be directly use the ➔ Are acellular positive strand mRNA due to genome has ➔ Although they are not cells, viruses are as negative strand ➔ diverse as the cells they infect, and different Class five has single stranded RNA, viruses are known to infect cells from all three transcription of the minus strand will provide domains of life. the positive strand mRNA will be Viruses are not domain complimented. ➔ Class six is a retrovirus and uses enzymes to form double stranded DNA, and use the negative strand to complement the mRNA. Cannot use directly the positive strand mRNA. Class Five and Six can only affect eukaryotes 1.5 MICROORGANISM AND THE BIOSPHERE Baltimore classification use genome of A BRIEF HISTORY OF LIFE ON EARTH viruses for classification (7 classification) ○ Same taxonomic rank ➔ Earth is about 4.6 billion years old, and ○ Only exclusive for viruses microbial cells first appeared between 3.8 and CLASS II and VI both single strand 4.3 billion years ago. ○ During central dogma, the goal of ➔ During the first 2 billion years of Earth’s virus is to have mRNA strand (will be existence, its atmosphere was anoxic (O2 was used to encode the protein) absent), and only nitrogen (N2), carbon dioxide ○ Class II, genome + strand, double (CO2), and a few other gasses were present. stranded (with compliment negative ➔ Only microorganisms capable of anaerobic strand), to make + strand mRNA+ metabolism could surve under these ○ Class VI has reverse transcription, conditions. Microorganisms will multiply and lead to evolution. ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 10  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ➔ Phototrophic bacteria produce oxygen (2) A BRIEF HISTORY OF LIFE ON EARTH ➔ Bacteria and archaea appeared first and eukarya appeared latter ➔ The timeline of life on Earth shows that 80% of ➔ LUKA (last universal ancestor) life’s history was exclusively microbial, and thus in many ways, Earth can be considered a microbial planet. ➔ All cellular organisms share certain characteristics and as a result, certain genes are found in all cells. ◆ FregenFor example, approximately 60 genes are universally present in cells of all three domains. ➔ Examination of these genes reveals that all three domains have descended from a common ancestor, the last universal common ancestor (LUCA) MICROBIAL ABUNDANCE & ACTIVITY IN THE BIOSPHERE ➔ Microorganisms are present everywhere on (1) A BRIEF HISTORY OF LIFE ON EARTH Earth that will support life ➔ They constitute a major fraction of global ➔ Early photographs lived in structures called biomass & are key reservoirs of nutrients microbial mats. essential for life ➔ PSB and GSB -> anoxygenic; Cyanobacteria -> ◆ Carbon major reservoir is plant due to oxygenic plant cell walls, proteins, RNA ◆ GSB - Green sulfur bacteria ◆ Nirogen reservoir is microbial ◆ PSB - Purple sulfur bacteria ◆ Phosphorus reservoir is microbial ◆ Due to photopigments cyanobacteria ➔ There are an estimated 2 x 1030 cells on Earth in the green layer ➔ PSB and GSB are capable of oxygenic phototrophs, they prefer anoxygenic ➔ Cyanobacteria prefer oxygen from photosynthesis ➔ Microbes are even abundant in habitats that are much too harsh for other forms of life- such microorganisms are called extremophiles ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 11  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 (2) MICROORGANISMS, AGRICULTURE AND HUMAN NUTRITION High = hyperthermophile Low = psychrophile Low pH = acidophile High pH = alkaliphile Pressure = barophile Salt plumbing = halophile 25% salt concentration ➔ Legumes live in close association with bacteria that form structures called nodules on their roots. 1.6 THE IMPACT OF MICROORGANISMS ◆ Inside the Nitrogenous fixing that ON HUMAN SOCIETY converted by microorganisms ◆ Nitrogen is held by three bond which is strong, not readily use by organisms (1) MICROORGANISMS AS AGENTS OF DISEASE To break it, nitrogenous fixing ➔ Death rates for the leading causes of death in does that work and converted the United States: 1900 and 2016 to ammonia and use by plants ◆ Influence, TB, gastro are leading death (like a fertilizer) to 1990 ➔ The digestive tract of ruminants has a large As compared today, the reason specialized chamber called the rumen in which due to lifestyle and things we cellulose is digested. intake ◆ Rumen is not able to produce the enzyme that will degrade cellulose. Need the help of the microorganism that can produce cellulose. ◆ Cellulose is highly present in plants. ◆ Microorganisms play an important role. ➔ Human enzymes lack the ability to break down complex carbohydrates (10-30 % of food energy) and so we rely on our gut microbiome for this purpose. ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 12  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ➔ Pure cultures are those that contain cells from only a single type of microorganism. ➔ Enrichment cultures techniques, which allow for the isolation from nature of microbes having particular metabolic characteristics, facilitate the discovery of diverse microorganisms. THE CONFLICT ➔ Spontaneous Generation Theory (Life emerges (3) MICROORGANISMS AND FOOD from non-living matter; “vital force” required) ◆ Life merges from nonliving matter ➔ Vs. ➔ Biogenesis Theory (“Life begets life”) ◆ New living organism from pre-existing life THE SPONTANEOUS GENERATION THEORY ➔ Francisco Redi (1668) ➔ Fermentation the product is Ethanol, Lactic Acid Propionic acid, and Acetic acid. (4) MICROORGANISMS AND INDUSTRY Challenge the spontaneous generation using meat Maggots came from eggs III MICROBIAL CULTIVATION EXPANDS Maggots could not happen in spontaneous THE HORIZON OF MICROBIOLOGY generation ➔ Aseptic technique is a collection of practices that allow for the preparation and maintenance ➔ John Needham (1745) of sterile (that is, without the presence of living organisms) nutrient media and solutions. ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 13 MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ➔ Result: no growth of microorganisms ➔ Spontaneous Generation supporters: strong acids and heat altered the air so it cannot support microbial growth. Briefly boiling broth mixture, cooling at a open container, microbes will grow days later. Flask will be sealed and microorganism grow Boiling time was kulang time, no enspore was eliminated Organic matter contained a viral forces ➔ Lazzaro Spallanzani (1768) ➔ George Friedrich Schröder & Theodor von Dusch (1850) ➔ Filtered air through sterile cotton wool Reviewed both scientist Concluded that heating bottle did not kill every bacteria Boiled one bottle sealed and unsealed Passing air via cotton plug Sealed no sign of life compare to other First one to use cotton plug Air was required for the vital force to work ➔ Result: no microbial growth ➔ Franz Schultze- passed air through strong acids ➔ Theodore Schwann - passed air through red-hot tubes ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 14